Incidental Mutation 'R6273:Rara'
ID 507484
Institutional Source Beutler Lab
Gene Symbol Rara
Ensembl Gene ENSMUSG00000037992
Gene Name retinoic acid receptor, alpha
Synonyms RARalpha1, RAR alpha 1
MMRRC Submission 044443-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6273 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 98818644-98865768 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 98861048 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 179 (T179A)
Ref Sequence ENSEMBL: ENSMUSP00000129791 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068133] [ENSMUST00000107473] [ENSMUST00000107474] [ENSMUST00000107475] [ENSMUST00000164748]
AlphaFold P11416
Predicted Effect probably benign
Transcript: ENSMUST00000068133
AA Change: T179A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: T179A

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000107473
AA Change: T176A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: T176A

DomainStartEndE-ValueType
low complexity region 54 77 N/A INTRINSIC
ZnF_C4 82 153 7.53e-40 SMART
HOLI 227 385 1.22e-34 SMART
low complexity region 422 433 N/A INTRINSIC
low complexity region 436 459 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000107474
AA Change: T179A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: T179A

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000107475
AA Change: T179A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: T179A

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000164748
AA Change: T179A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: T179A

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Meta Mutation Damage Score 0.0712 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.0%
  • 20x: 94.2%
Validation Efficiency 98% (78/80)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for targeted null mutations show high neonatal mortality due to maternal cannibalization, failure to thrive, and excess mortality during the postnatal period. Male survivors exhibit testicular degeneration. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik T A 5: 64,055,561 (GRCm39) I99N probably damaging Het
Ank3 G A 10: 69,838,395 (GRCm39) R1566K possibly damaging Het
Ankrd31 A G 13: 96,988,181 (GRCm39) I1065V possibly damaging Het
Aox1 A G 1: 58,378,831 (GRCm39) T1027A probably benign Het
Atm G A 9: 53,399,222 (GRCm39) P1593L probably benign Het
Atp13a5 T G 16: 29,167,555 (GRCm39) I132L probably benign Het
BC035044 A G 6: 128,867,852 (GRCm39) probably benign Het
Cadm3 CT C 1: 173,176,691 (GRCm39) probably benign Homo
Car3 C T 3: 14,936,677 (GRCm39) P247S probably benign Het
Ccdc7a T C 8: 129,513,819 (GRCm39) Y160C probably damaging Het
Cd1d1 A G 3: 86,905,564 (GRCm39) V143A probably benign Het
Cemip2 T A 19: 21,779,369 (GRCm39) V393E probably damaging Het
Cog6 A T 3: 52,903,473 (GRCm39) F142I probably damaging Het
Cracd A T 5: 77,005,568 (GRCm39) D643V unknown Het
Crhr1 T G 11: 104,054,682 (GRCm39) N98K possibly damaging Het
Csf1 A G 3: 107,656,479 (GRCm39) V72A probably damaging Het
Cwc15 T A 9: 14,421,537 (GRCm39) I201K probably benign Het
Dgka T C 10: 128,559,515 (GRCm39) K482R probably benign Het
Dnah7b T C 1: 46,281,476 (GRCm39) S2846P possibly damaging Het
Dst T A 1: 34,314,347 (GRCm39) I4199N probably damaging Het
Dusp7 A G 9: 106,251,095 (GRCm39) T407A possibly damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Fem1a T C 17: 56,564,083 (GRCm39) Y59H possibly damaging Het
Fetub C T 16: 22,751,081 (GRCm39) R143C probably damaging Het
Filip1 A T 9: 79,723,168 (GRCm39) D1150E probably benign Het
Gabra1 A G 11: 42,031,138 (GRCm39) V264A probably damaging Het
Gm4131 T C 14: 62,702,299 (GRCm39) E223G probably damaging Het
Gon4l T C 3: 88,763,156 (GRCm39) V333A probably damaging Het
Gsk3b A G 16: 38,028,408 (GRCm39) T289A probably benign Het
Hmcn2 T C 2: 31,301,846 (GRCm39) S2912P probably damaging Het
Htr7 A T 19: 36,018,969 (GRCm39) probably benign Het
Ibsp A G 5: 104,458,167 (GRCm39) T235A probably benign Het
Ints13 A T 6: 146,467,179 (GRCm39) D116E probably damaging Het
Irag1 G T 7: 110,470,790 (GRCm39) H848N probably benign Het
Kctd19 T C 8: 106,112,117 (GRCm39) N753S probably benign Het
Mdn1 A G 4: 32,715,979 (GRCm39) N2054D probably benign Het
Mink1 A T 11: 70,502,261 (GRCm39) K880* probably null Het
Myo15b T A 11: 115,753,625 (GRCm39) L824Q possibly damaging Het
Napepld T C 5: 21,870,320 (GRCm39) E366G probably benign Het
Obscn T A 11: 58,967,819 (GRCm39) T2662S possibly damaging Het
Or2g7 T G 17: 38,378,686 (GRCm39) L208R probably damaging Het
Or2n1b T A 17: 38,459,833 (GRCm39) M118K possibly damaging Het
Or4k52 T C 2: 111,611,567 (GRCm39) F301L probably benign Het
Or52p1 A G 7: 104,267,102 (GRCm39) D72G probably damaging Het
Or5b12 A G 19: 12,896,764 (GRCm39) V303A probably benign Het
Or6d13 A G 6: 116,518,277 (GRCm39) T288A possibly damaging Het
Pah T C 10: 87,412,077 (GRCm39) probably null Het
Panx3 T G 9: 37,578,725 (GRCm39) I85L probably benign Het
Pate4 T C 9: 35,519,086 (GRCm39) N94D probably benign Het
Pde4d A G 13: 110,086,755 (GRCm39) M610V possibly damaging Het
Pik3c2b T C 1: 132,994,449 (GRCm39) S138P probably benign Het
Pkn1 T C 8: 84,398,899 (GRCm39) N696S probably damaging Het
Plppr2 A G 9: 21,855,801 (GRCm39) E258G probably damaging Het
Plxnd1 A T 6: 115,955,453 (GRCm39) M538K probably damaging Het
Prepl G T 17: 85,390,696 (GRCm39) N87K probably benign Het
Prkag2 C A 5: 25,152,534 (GRCm39) R190L probably damaging Het
Rfx7 A G 9: 72,524,279 (GRCm39) K490E possibly damaging Het
Rgsl1 C T 1: 153,703,211 (GRCm39) V147M possibly damaging Het
Rph3a A G 5: 121,083,485 (GRCm39) I595T possibly damaging Het
Rsf1 CG CGACGGCGGTG 7: 97,229,115 (GRCm39) probably benign Homo
Slc35e2 C T 4: 155,694,483 (GRCm39) P10L probably benign Het
Slc8a2 T C 7: 15,879,259 (GRCm39) F582L possibly damaging Het
Sprr2e A G 3: 92,260,171 (GRCm39) M1V probably null Het
Steap1 T A 5: 5,790,827 (GRCm39) R40S possibly damaging Het
Tbc1d2 C T 4: 46,629,912 (GRCm39) G252R probably benign Het
Thsd7a A T 6: 12,408,835 (GRCm39) V729E probably damaging Het
Tmprss13 A G 9: 45,256,630 (GRCm39) Y525C probably damaging Het
Tnik A T 3: 28,631,649 (GRCm39) H383L possibly damaging Het
Vars1 T C 17: 35,232,719 (GRCm39) L881S probably damaging Het
Vmn1r201 A C 13: 22,659,385 (GRCm39) S200R probably damaging Het
Vmn2r130 A T 17: 23,295,759 (GRCm39) H643L probably benign Het
Vmn2r14 A T 5: 109,369,133 (GRCm39) W147R probably benign Het
Vps53 T C 11: 75,992,844 (GRCm39) E367G probably benign Het
Xab2 C T 8: 3,661,822 (GRCm39) G544S probably damaging Het
Ythdf3 T A 3: 16,259,020 (GRCm39) V400E possibly damaging Het
Zfand5 C T 19: 21,257,060 (GRCm39) P147S probably benign Het
Zfp768 A T 7: 126,944,319 (GRCm39) probably null Het
Zswim8 A G 14: 20,763,521 (GRCm39) M423V probably benign Het
Other mutations in Rara
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00951:Rara APN 11 98,858,992 (GRCm39) missense probably benign 0.00
IGL01155:Rara APN 11 98,859,010 (GRCm39) missense possibly damaging 0.92
IGL02141:Rara APN 11 98,858,907 (GRCm39) missense probably damaging 1.00
IGL03194:Rara APN 11 98,862,490 (GRCm39) missense possibly damaging 0.96
annie UTSW 11 98,864,452 (GRCm39) missense unknown
kane UTSW 11 98,862,595 (GRCm39) missense probably damaging 1.00
Orphan UTSW 11 98,860,989 (GRCm39) missense probably damaging 1.00
warbucks UTSW 11 98,861,395 (GRCm39) missense probably damaging 1.00
PIT4486001:Rara UTSW 11 98,864,321 (GRCm39) missense possibly damaging 0.88
R0626:Rara UTSW 11 98,862,406 (GRCm39) critical splice acceptor site probably null
R1973:Rara UTSW 11 98,862,496 (GRCm39) missense possibly damaging 0.91
R3975:Rara UTSW 11 98,861,395 (GRCm39) missense probably damaging 1.00
R4357:Rara UTSW 11 98,858,937 (GRCm39) missense probably damaging 0.98
R5102:Rara UTSW 11 98,857,185 (GRCm39) missense possibly damaging 0.80
R5147:Rara UTSW 11 98,841,550 (GRCm39) missense probably benign 0.35
R5381:Rara UTSW 11 98,862,410 (GRCm39) missense possibly damaging 0.93
R5570:Rara UTSW 11 98,863,478 (GRCm39) missense probably damaging 1.00
R5861:Rara UTSW 11 98,858,987 (GRCm39) nonsense probably null
R6404:Rara UTSW 11 98,851,839 (GRCm39) missense probably benign 0.16
R8906:Rara UTSW 11 98,860,989 (GRCm39) missense probably damaging 1.00
R8921:Rara UTSW 11 98,864,452 (GRCm39) missense unknown
R8978:Rara UTSW 11 98,862,595 (GRCm39) missense probably damaging 1.00
R9224:Rara UTSW 11 98,857,236 (GRCm39) frame shift probably null
R9476:Rara UTSW 11 98,860,983 (GRCm39) missense probably benign 0.02
R9510:Rara UTSW 11 98,860,983 (GRCm39) missense probably benign 0.02
Predicted Primers PCR Primer
(F):5'- ATGAGTCAGACAGGTTAGTGTG -3'
(R):5'- TCCTGACAGTGTAGGAGGAG -3'

Sequencing Primer
(F):5'- CACTGTTTTGTGGATCTGTCTGTC -3'
(R):5'- CTGACAGTGTAGGAGGAGACAGG -3'
Posted On 2018-03-15